Amino Acids

For a general introduction to amino acids, please see Amino Acids in Wikipedia.

20 Standard Amino Acids and Mnemonics
Here are the names of the twenty standard amino acids, with their three and one-letter abbreviations. Mnemonic names are intended to help you to remember the one-letter codes, but are not the correct names.

Unusual Amino Acids
Post-translational modifications of amino acids include phosphorylation and nitrosylation, e.g. to produce nitrotyrosine. However, there are at least two non-standard amino acids that are genetically encoded, discussed below.

Selenocysteine: the 21st amino acid
Rare proteins in all domains of life include selenocysteine (Sec, U). Over a dozen entries in the PDB include selenocysteine, identified as CSE.

Pyrrolysine: the 22nd amino acid
Some proteins in methanogenic archaea include pyrrolysine (Pyl). Methanosarcina barkeri monomethylamine methyltransferase (MtmB, 1nth, 1l2q) was the first identified structure containing this amino acid, and in the crystal structure it is identified as BGX, with the rest of the amnio acid identified as LYS202. Chemically modified forms of pyrrolysine are present in 1tv2, 1tv3, and 1tv4. The PDB also contains several structures for pyrrolysyl-tRNA synthetase.

No 23rd amino acid?
The 21st and 22nd amino acids are specified by the stop codons UGA and UAG respectively, modified with downstream stem-loop structures in the mRNA. Lobanov et al. searched "16 archaeal and 130 bacterial genomes for tRNAs with anticodons corresponding to the three stop signals". Their data suggest that "the occurrence of additional amino acids that are widely distributed and genetically encoded is unlikely."

Structure, Properties, Behaviors in Proteins
Angel Herráez has provided a tutorial introduction to amino acid structure in which each of the 20 amino acids may be visualized in 3D using Jmol.

Please help to expand the list below to include all 20 amino acids.

Histidine
His H: Charged: Basic, Aromatic, Bulky

See Histidine in Wikipedia, where the structure is shown. The sidechain of His can be positively charged (protonated), in which case both of the nitrogens in the sidechain imidazole ring have hydrogens, and the charge is delocalized between them. The pKa for protonation is 6.1. This means that, on average at any moment, half of the His sidechains are protonated when the pH is 6.1. At the pH of blood, 7.4 ±0.05, His sidechains are positively charged less than 10% of the time. Therefore, His is not included in the usual list of positively charged amino acids (lysine and arginine).

Phenylalanine
Phe F: Neutral, Aromatic, Bulky

See Phenylalanine in Wikipedia, where the structure is shown. Phe participates in Cation-pi interactions. Phenylketonuria is a genetic disease in which the enzyme that converts phenylalanine to tyrosine is nonfunctional, leading to toxicity from excess phenylalanine, and tyrosine deficiency.

Tryptophan
Trp W: Neutral, Polar, Aromatic, Bulky

See Tryptophan in Wikipedia, where the structure is shown. In trans-membrane proteins, tryptophans often lie at the interface between water and lipid. An example is the potassium channel, e.g. 1bl8. To see their positions, use the Find dialog in FirstGlance in Jmol. Trp participates in Cation-pi interactions.

Tyrosine
Tyr Y: Neutral, Polar, Aromatic, Bulky

See Tyrosine in Wikipedia, where the structure is shown, and Nitrotyrosine. Tyr participates in Cation-pi interactions.